Well the shift thing is going to be an issue with your trans not the motor. Sounds like you've got the trans cable not adjusted right. I'm assuming you have an aod? If that's not adjusted properly your going to be shifting way sooner than necessary and prolly missing out on a good part of your power band. Now the shaking is another matter and I suspect it's linked to the firing order being played with.
04 3.9l Convertible- Daily driver
94 5.0l Convertible- Work in progress
92 5.0l Hatchback- Another work in progress